The diversity of fungal species comprising the lung mycobiome is a reflection of exposure to ubiquitous environmental and endogenous filamentous fungi and yeasts. Most lung mycobiome studies have been culture-based. A few have utilized next generation sequencing (NGS). Despite the low number of published NGS studies, several themes emerge from the literature: (1) moulds and yeasts are present in the human respiratory tract, even during health; (2) the fungi present in the respiratory tract are highly variable between individuals; and (3) many diseases are accompanied by decreased diversity of fungi in the lungs. Even in patients with the same disease, different patients have been shown to harbour distinct fungal communities. Those fungal species present in any one individual may represent a patient’s unique environmental exposure(s), either to species restricted to the indoor environment, for example Penicillium, or species found in the outdoor environment such as Aspergillus, wood and vegetation colonizing fungi and plant pathogens. In addition to causing clinical fungal infections, the lung mycobiome may have profound inflammatory effects that can cause or worsen lung disease. Most diseases that have been studied, including cystic fibrosis, asthma, lung transplant, COPD and bronchiectasis, have been associated with decreases in fungal diversity. However, none of these diversity studies distinguish between accidental, transient fungal colonisers and true residents of the respiratory tract.
Where does Aspergillus feature in the mycobiomes of the respiratory tract? Do these mycobiomes reflect the diversity of fungi in outdoor and internal environments? These intriguing questions are explored here. Even though Aspergillus is ubiquitous in many global environments its role in a number of respiratory diseases is not clear.